Is STAT2 p.Pro489His (c.1466C>A) pathogenic?

STAT2 p.Pro489His (c.1466C>A) is classified Uncertain significance in STAT2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-12). AlphaMissense: likely benign (0.2312); Ultra-rare (popmax 0.0165%, mid); Associated with primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection.

How common is STAT2 p.Pro489His (c.1466C>A) in the general population?

STAT2 p.Pro489His (c.1466C>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about STAT2 p.Pro489His (c.1466C>A)?

AlphaMissense predicts likely benign (score 0.2312) — an in-silico prediction, not a clinical call.

STAT2 p.Pro489His

Q: What condition is associated with STAT2 p.Pro489His (c.1466C>A)?

STAT2 p.Pro489His (c.1466C>A) is associated with primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection (ClinVar).

Q: How is Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1466C>A · rs138681270 · VCV845773

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2312 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection

Computational evidence

Protein change
AlphaMissense	0.2312	likely benign
REVEL	0.407	indeterminate
SaProt	LLR -12.84	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP 5.8	GERP 0.69, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 13 kb · p 6.2e-18 · regional, not allelic
Overall
CADD	22.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,060 alleles

Filtering AF 0.00662% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00533%

Overall 0.00651% 105/1,613,662 alleles · ultra-rare exomes 92/1,461,374 · genomes 13/152,288 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,060
Admixed American	0.0133%	7,495
Remaining individualsnot grpmax-eligible	0.0096%	10,416
European (non-Finnish)	0.00704%	14,214
East Asian	0.00446%	22,434
South Asian	0.0044%	22,751
African / African-American	0.00133%	75,042

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: STAT2
Protein: p.Pro489His
Coding: c.1466C>A
MANE Select: NM_005419
dbSNP: rs138681270
Type: single nucleotide variant
Location: chr12:56349034 (GRCh38)
Gene constraint: LOEUF 0.497 · pLI 0.81 (gnomAD)
Structure: AlphaFold pLDDT 78.45 · 6 PDB
Residue 489: the 'mediates interaction with usp18' region; the 'interaction with heartland virus nss' region; an α-helix

Full STAT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

STAT2 p.Pro489Arg Uncertain significance ★★ ⚠ same residue
STAT2 p.Pro489Leu Uncertain significance ★★ ⚠ same residue
STAT2 p.Pro489Ala Uncertain significance ★ ⚠ same residue
STAT2 p.Pro489Thr Uncertain significance ★ ⚠ same residue
STAT2 p.Arg667Ter Pathogenic/Likely pathogenic ★★ same condition
STAT2 p.Gln274Ter Pathogenic/Likely pathogenic ★★ same condition
STAT2 p.Ala219Thr Uncertain significance ★★ ⚠ same condition
STAT2 p.Ala302Thr Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/stat2-p-pro489his (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown